From 31ed4aa34263b5afdadd50020609e318d235be8b Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@stud.unibas.ch>
Date: Fri, 26 Oct 2012 10:29:26 +0200
Subject: [PATCH] First search for blastall instead for blastp to make it run
on the BC2 environment. The problem is, that wu-blast gets called when
calling blastp.
---
modules/bindings/pymod/blast.py | 19 ++++++++++---------
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index 9fdc739cf..73fe18754 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -144,12 +144,13 @@ def CreateDB(infasta, dbout, mkdb_cmd=None):
"""
if mkdb_cmd==None:
try:
- exe=settings.Locate('makeblastdb')
- args=[exe, '-in', infasta, ' -max_file_sz 10GB -out', dbout,'-dbtype','prot']
+ exe=settings.Locate('formatdb')
+ args=[exe, '-i', infasta, '-v',str(10000),'-n',dbout]
except:
try:
- exe=settings.Locate('formatdb')
- args=[exe, '-i', infasta, '-v',str(10000),'-n',dbout]
+ exe=settings.Locate('makeblastdb')
+ args=[exe, '-in', infasta, ' -max_file_sz 10GB -out', dbout,'-dbtype','prot']
+
except:
raise RuntimeError('could not find makeblastdb/formatdb executable')
else:
@@ -172,10 +173,10 @@ def BlastVersion(blast_location=None):
"""
try:
- blast_exe=settings.Locate('blastp',explicit_file_name=blast_location)
+ blast_exe=settings.Locate('blastall',explicit_file_name=blast_location)
except:
try:
- blast_exe=settings.Locate('blastall', explicit_file_name=blast_location)
+ blast_exe=settings.Locate('blastp', explicit_file_name=blast_location)
except:
raise RuntimeError('could not find blast executable')
@@ -233,12 +234,12 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
if blast_location==None:
try:
- blast_exe=settings.Locate('blastp')
+ blast_exe=settings.Locate('blastall')
except:
try:
- blast_exe=settings.Locate('blastall')
+ blast_exe=settings.Locate('blastp')
except:
- raise BlastError('could not find blast executable')
+ raise RuntimeError('could not find blast executable')
else:
blast_exe=settings.Locate(os.path.basename(blast_location),explicit_file_name=blast_location)
--
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